Putting a diode on one cell would prevent it from ever charging.If for some reason the voltages are not equal (in the real world they won't be exactly equal) and I put a diode on the less powerful battery to protect it - will (if the diode starts to have a reverse polarity) the weaker battery also be unable to conduct electricity to the motor because the diode is reserved biased?
If the two cells are at different voltages when you want to put them in parallel, charge the lower one until they are the same. Once in parallel, they can never be at different voltages again.
Bob